Uncovering new toxicities from chronic non-rodent studies

Preclinical toxicology studies are an essential part of the drug discovery-development pipeline, to support the safe conduct of clinical trials. And drug safety is, of course, one of the most critical aspects to ensure during drug development.

We were pleased to see the recent publication by Merck on a text-mining approach to assess the value of chronic non-rodent toxicology studies. 

Preclinical safety assessment groups employ a variety of animal models and assays to satisfy regulatory agency requirements to identify and characterize drug toxicities, describe drug exposures, and provide qualitative and quantitative risk assessments for human exposure. These require considerable resource investment, however the results are often “locked away” in internal reports. This means re-use of these valuable data is difficult and costly.

This is a common situation within the pharmaceutical industry – where critical information is locked away in textual reports, such as the informed scientific conclusions of pathologists, histologists, safety experts. Natural language processing can overcome the barriers, extracting structured facts from unstructured documents, and Merck’s paper describes an evaluation of a text mining workflow to access these important data.


Press Release: Natural Language Processing (NLP) to Optimize Clinical Trials: I2E Hackathon at the Linguamatics Text Mining Summit - Using text mining to address healthcare information challenges


Enhancing problem list reconciliation with Natural Language Processing (NLP): Improve patient care quality with population health text mining analytics

The shift from volume to value-based compensation is driving provider demand for better insights into the health of patient populations. Providers recognize that access to more complete patient data can enhance their ability to deliver cost-effective care and high quality outcomes. This is especially true for patients with multiple chronic conditions, who typically have more complicated care needs and higher hospital utilization rates.

Figure 1 High risk patients are frequently suffering from complex comorbidities

Typically, physicians refer to problem lists when assessing a patient’s health and evaluating treatment alternatives. Problem lists rely on coded disease states and offer a concise view of a patient’s medical issues. Unfortunately, these lists are often incomplete or out of date. Consider, for example, a patient who is referred to an orthopedic surgeon for a broken wrist. If the problem list only includes details of the wrist injury, the physician may not be immediately aware of underlying chronic conditions, such as diabetes, that could impact the best course of treatment and outcomes.


Last week I attended the Cambridge Rare Disease Network (CRDN) 2016 SummitCRDN is a newly established charity working to build a community of people in Cambridge to address the unmet needs in rare disease research and treatment. As last year, there was a great set of speakers, from patient groups, academia, pharma/biotech and vendors.

There has been a step-change in awareness within the pharma industry in the last decade, with an increasing interest and investment in tackling rare diseases. I blogged last year about an interview with Patrick Vallance on this same topic.  He gave several reasons why GSK are interested in rare disease, and these three reasons all were echoed by the CRDN speakers.

The topmost of these reasons was given most clearly by speakers from patient groups, such as Daniel Lewi from the Cure & Action for Tay-Sachs (CATS) Foundation, Karen Harrison from ALD Life, and Emily Kramer-Kolingoff, from Emily’s Entourage. They spoke of the huge impact that rare disease has on individuals and families, and the urgent need for research into new or repurposed treatments for the 1 in 17 people affected by a rare disease.


Linguamatics are delighted once more to sponsor the Findacure Student Voice Essay Competition. Findacure is a UK charity that is building the rare disease community to drive research and develop treatments.   

The winning essay will be published in the Orphanet Journal of Rare Diseases, and the essay topics are:

  1. The impact of a rare disease is much more widespread than its direct symptoms. Discuss how, with particular reference to the patient experience.
  2. How can rare diseases lead the way in medical research and clinical innovation?
  3. How can clinicians and researchers, including students, help to deliver the UK Strategy for Rare Diseases?

One of the big challenges for the development of treatments for rare disease is the need for a thorough understanding of the natural history of each of the 7000 currently known rare diseases. It’s critical to have detailed systematic information on both the genotypic aspect (the genes and mutations), and the phenotypic aspect (pathways involved or disrupted, symptom severities, etc.).